Chromosome-scale genome assembly of bread wheat’s wild relative Triticum timopheevii

Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Wheat’s wild relative species provide a hugely untapped reservoir of genetic diversity for wheat improvement. Triticum timopheevii (2n = 4x = 28) is a tetraploid wheat wild relative species containing the At and G genomes that has been exploited in many wheat pre-breeding programmes over the last few decades. In this study, we report the generation of a chromosome-scale reference genome assembly of T. timopheevii accession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The total assembly size was 9.35 Gb with a contig N50 of 42.4 Mb. In total, 166,325 gene models were predicted. Comparative genome analysis confirmed previously known chromosomal translocations and indicated new chromosome rearrangements. Analysis of the genomic distribution of DNA methylation showed that the G genome had on average more methylated..., , , # **Chromosome-scale genome assembly of bread wheat’s wild relative *Triticum timopheevii***

**Assembly**\
Pseudomolecules assembled with Hifiasm and Salsa2 and organelle genome scaffolds assembled with Oatk (

* Timopheevii.final.pm.oriented.with_org.fasta.gz (assembly with organellar genomes)
* Timopheevii.final.pm.oriented.fasta.gz (assembly of only nuclear chromosomes)

Hi-C Contact map generated by mapping short-reads using the Arima pipeline ( and scaffolds manually curated with Rapid Curation Pipeline (

* Timopheevii.final.pm.oriented.pretext
* This is the final HiC contact map generated by mapping the HiC short reads onto the curated assembly. This file can be opened using PretextView v.0.2.5 (available at

**Annotation**\
Gene models were generated from the Timopheevii.final.pm.oriented.fasta assembly using REAT - Robust and Extendable eukaryotic Annotation Toolkit and Minos which make use of Mikado , Portcullis and many third party tools (listed in the abov...